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Evolution of Spliceosomal snRNA Genes in Metazoan Animals

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Abstract

While studies of the evolutionary histories of protein families are commonplace, little is known on noncoding RNAs beyond microRNAs and some snoRNAs. Here we investigate in detail the evolutionary history of the nine spliceosomal snRNA families (U1, U2, U4, U5, U6, U11, U12, U4atac, and U6atac) across the completely or partially sequenced genomes of metazoan animals. Representatives of the five major spliceosomal snRNAs were found in all genomes. None of the minor splicesomal snRNAs were detected in nematodes or in the shotgun traces of Oikopleura dioica, while in all other animal genomes at most one of them is missing. Although snRNAs are present in multiple copies in most genomes, distinguishable paralogue groups are not stable over long evolutionary times, although they appear independently in several clades. In general, animal snRNA secondary structures are highly conserved, albeit, in particular, U11 and U12 in insects exhibit dramatic variations. An analysis of genomic context of snRNAs reveals that they behave like mobile elements, exhibiting very little syntenic conservation.

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Notes

  1. See http://www.bioinf.uni-leipzig.de/Publications/SUPPLEMENTS/08-001/.

  2. See http://www.sanger.ac.uk/Users/td2/pecan-CAF1.

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Acknowledgments

This work was supported in part by the Graduierten-Kolleg Wissensrepräsentation and by the Bioinformatics Initiative of the Deutsche Forschungs-Gemeinschaft (DFG). Special thanks go to Petra Pregel and Jens Steuck for making the work much easier.

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Authors and Affiliations

  1. Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstrasse 16-18, 04107, Leipzig, Germany

    Manuela Marz & Peter F. Stadler

  2. Interdisziplinäres Zentrum für Bioinformatik, University of Leipzig, Härtelstrasse 16-18, 04107, Leipzig, Germany

    Toralf Kirsten & Peter F. Stadler

  3. RNomics Group, Fraunhofer Institute for Immunology and Cell Therapy, Perlickstr. 1, Leipzig, Germany

    Peter F. Stadler

  4. Institute for Theoretical Chemistry and Structural Biology, University of Vienna, Währingerstrasse 17, 1090, Wien, Austria

    Peter F. Stadler

  5. The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA

    Peter F. Stadler

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  1. Manuela Marz
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Marz, M., Kirsten, T. & Stadler, P.F. Evolution of Spliceosomal snRNA Genes in Metazoan Animals. J Mol Evol 67, 594–607 (2008). https://doi.org/10.1007/s00239-008-9149-6

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